There was a time not that long ago when it was easy to tell the difference between viruses and the rest of life. Most obviously, viruses were tiny and genetically simple. The influenza virus, for example, measures about 100 nanometers across, and has just 13 genes.

Those two standards, it’s now clear, belong in the trash. Over the past decade, scientists have discovered a vast menagerie of viruses that are far bigger, and which carry enormous arsenals of genes. French researchers are now reporting the discovery of the biggest virus yet. The pandoravirus, as they’ve dubbed it, is 1,000 times bigger than the flu virus by volume and has nearly 200 times as many genes — 2,556 all told.

Making the discovery all the more startling is the fact that, of all the genes that pandoraviruses carry, only six percent match any gene known to science.

“We believe we’re opening a Pandora’s box – not so much for humanity but for dogma about viruses,” said Dr. Jean-Michel Claverie of the University of Mediterranée, co-author of the paper that was published online Thursday in the journal Science. “We believe we’re touching an alternative tree of life.”

Giant viruses would be important enough simply for the way they have blurred the line between viruses and the rest of life. But they excite scientists for another reason. Utterly unknown a decade ago, they turn out to be everywhere, including in our own bodies. What effect they have on the world’s ecosystem — or our own health — is anyone’s guess right now.

It was the very giant-ness of giant viruses that allowed them to be overlooked for so long. Scientists first discovered viruses in the late 1800s when they were puzzled by a disease that beset tobacco plants. They mashed up wilted tobacco leaves with water and passed the mixture through fine porcelain filters that trapped bacteria and fungi. The clear liquid could still make healthy tobacco leaves sick. The Dutch botanist Martinus Beijerinck dubbed it “a contagious living fluid.”

In the 1930s, the invention of powerful microscopes finally allowed scientists to see viruses. They found that viruses were unlike ordinary cells: they didn’t generate their own fuel; they didn’t grow or divide. Instead, viruses invaded cells, hijacking their biochemistry to make new copies of themselves. Being small and simple seemed like part of the viral way of life, allowing them to replicate fast.

It wasn’t until 2003 that a team of French researchers discovered the first giant virus. They had been puzzling over sphere-shaped objects that were the size of bacteria but contained no bacterial DNA. Eventually they realized that they were looking at a monstrously oversized virus, containing 979 genes.

Those first giant viruses were isolated from amoebae living in water from a cooling tower. Once scientists realized that viruses could be so large, they changed their search parameters and started finding other species in all manner of places, from swamps to rivers to contact lens fluid.

And along the way the biggest viruses got bigger. In 2011, Dr. Claverie and his colleagues set a new record with megaviruses, a type of giant virus with 1,120 genes they discovered in sea water off the coast of Chile. They then dug into the sediment below that sea water and discovered pandoravirsues, with more than twice as many genes.

Dr. Claverie speculates that pandoraviruses and other giant viruses evolved from free-living microbes that branched off from other life several billion years ago. “The type of cells they may have evolved from may have disappeared,” he said.

The idea that giant viruses represent separate branches on the tree of life is a controversial one that many other experts aren’t ready to embrace. “They provide no evidence for that notion, so it seems a distraction to me,” said T. Martin Embley, a professor of evolutionary molecular biology at Newcastle University.

Despite those reservations, Dr. Embley and other researchers hail pandoraviruses as an important discovery. “I think it’s wonderful that such crazy and divergent lifeforms continue to be discovered,” said Tom Williams, Dr. Embley’s colleague at Newcastle University.

The new study also drives home the fact that giant viruses are far from rare. Shortly after discovering pandoraviruses in sea floor sediment, Dr. Claverie and his colleagues found them in water from a lake in Australia, 10,000 miles away. “It definitely indicates that they must not be rare at all,” said Dr. Claverie.

Giant viruses may be so common, in fact, that they may be hiding inside of us, too. In a paper published online on July 2 in The Journal of Infectious Diseases, French researchers offered evidence that giant viruses dwell in healthy people. They isolated a new giant virus from blood donated by a healthy volunteer, and then found antibodies and other signs of the virus in four other donors.

Giant viruses may lurk harmlessly in our bodies, invading the amoebae we harbor. Whether they can make us sick is an open question. “I don’t believe we have the proof at the moment that these viruses could infect humans,” said Dr. Claverie.

“But again,” he added, “never say never.”

That’s wise advice when it comes to giant viruses.

Copyright 2013 The New York Times Company. Reproduced with permission.